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Table 4 Top SNPs identified by the Random Forest and GRAMMAR-CG Approach for trait 3

From: Genome wide association analysis of the 16th QTL- MAS Workshop dataset using the Random Forest machine learning approach

   

Trait 3

    

Multiple Trait EBV

 

Multiple Trait EBV

 

SNP name

CHR

Pos Kb

 

SNP name

CHR

Pos Kb

 

SNP4738

3

36.850

 

SNP3585

2

79.200

1,54E-22

SNP3585

2

79.200

 

SNP4738

3

36.850

1,71E-14

SNP1683

1

84.100

 

SNP4044

3

2.150

1,52E-13

SNP3584

2

79.150

 

SNP1682

1

84.050

5,52E-13

SNP1291

1

64.500

 

SNP1683

1

84.100

7,06E-11

SNP1478

1

73.850

 

SNP3584

2

79.150

9,54E-11

SNP1682

1

84.050

 

SNP1699

1

84.900

8,86E-08

SNP1169

1

58.400

 

SNP1166

1

58.250

3,33E-06

Single Trait EBV

 

Single Trait EBV

 

RanFoG

 

Trait 3 ST

 

GRAMMAR

Trait 3 ST

 

SNP1683

1

84.100

 

SNP1682

1

84.050

7,61E-13

SNP4738

3

36.850

 

SNP1683

1

84.100

1,12E-12

SNP7012

4

50.550

 

SNP3585

2

79.200

1,36E-11

SNP1291

1

64.500

 

SNP4044

3

2.150

9,75E-09

SNP1169

1

58.400

 

SNP1699

1

84.900

2,41E-08

SNP1478

1

73.850

 

SNP1161

1

58.000

1,61E-07

SNP296

1

14.750

 

SNP4738

3

36.850

2,28E-06

SNP3585

2

79.200

 

SNP1178

1

58.850

1,43E-05

SNP4317

3

15.800

 

SNP4047

3

2.300

2,39E-05

SNP295

1

14.700

 

SNP3584

2

79.150

2,80E-05

Yield Deviation

 

Yield Deviation

 

SNP1683

1

84.100

 

SNP1682

1

84.050

2,49E-19

SNP1682

1

84.050

 

SNP1683

1

84.100

2,09E-18

SNP4738

3

36.850

 

SNP3585

2

79.200

5,84E-15

SNP3585

2

79.200

 

SNP1699

1

84.900

3,29E-12

SNP295

1

14.700

 

SNP4044

3

2.150

3,88E-08

SNP1161

1

58.000

 

SNP1161

1

58.000

6,46E-08

SNP1169

1

58.400

 

SNP3584

2

79.150

8,54E-08

SNP296

1

14.750

 

SNP4738

3

36.850

2,30E-07

SNP278

1

13.850

 

SNP1166

1

58.250

1,86E-06

SNP1166

1

58.250

 

SNP1697

1

84.800

1,92E-06

    

SNP1178

1

58.850

3,32E-06

    

SNP1168

1

58.350

7,79E-06

    

SNP1685

1

84.200

1,42E-05

    

SNP3595

2

79.700

2,08E-05

    

SNP4047

3

2.300

3,11E-05

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